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The precise evaluation of the system design and characteristics is a challenge for experts and engineers. This paper considers the problem of the development and application of a digital twin to assess cyberphysical systems. We analyze the details of digital twin applications at different lifecycle stages. The work reviews and summarizes properties of models concerning the digital and physical components of a cyberphysical system (CPS). The other issue of a CPS is increasing cybersecurity threat for objects, so special attention is paid to the heterogeneous digital twin usage scenarios to improve CPS cybersecurity. The article also details the heterogeneous digital twin’s implementation for a real upper-level control system of a nuclear power plant. The presented heterogeneous digital twin combines virtual machines with real equipment, namely hardware-in-the-loop (HiL) components. The achievements and drawbacks of the implemented model, including single timescale maintaining challenges, are discussed.